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- PDB-6nfl: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with... -

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Basic information

Entry
Database: PDB / ID: 6nfl
TitleCrystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G complexed with 2-HP
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / APOBEC / deaminase
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
APOBEC-like C-terminal domain / Novel AID APOBEC clade 2 / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
pyrimidin-2-ol / 1,3-diazinan-2-one / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.731 Å
AuthorsShi, K. / Orellana, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Faseb Bioadv / Year: 2020
Title: Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B
Authors: Shi, K. / Demir, O. / Carpenter, M.A. / Banerjee, S. / Harki, D.A. / Amaro, R.E. / Harris, R.S. / Aihara, H.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2637
Polymers22,8451
Non-polymers4186
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 50.650, 149.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 22844.803 Da / Num. of mol.: 1
Mutation: F200S, W228S, L230K, Y250S, F308K, Y315D, D316Q, P317G, L318R, Y319C, K320Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UH17, single-stranded DNA cytosine deaminase

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-L60 / 1,3-diazinan-2-one


Mass: 100.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O
#3: Chemical ChemComp-71O / pyrimidin-2-ol


Mass: 96.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 21113 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.1
Reflection shellResolution: 1.73→1.78 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / Num. measured obs: 12773 / Num. unique all: 2077 / CC1/2: 0.639 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3366: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQK

5cqk


Resolution: 1.731→41.909 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1051 5.09 %
Rwork0.1623 --
obs0.1639 20663 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.731→41.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 27 134 1663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041613
X-RAY DIFFRACTIONf_angle_d0.7142184
X-RAY DIFFRACTIONf_dihedral_angle_d20.772957
X-RAY DIFFRACTIONf_chiral_restr0.045220
X-RAY DIFFRACTIONf_plane_restr0.004291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7313-1.81010.29331240.24282257X-RAY DIFFRACTION92
1.8101-1.90550.25021420.20742319X-RAY DIFFRACTION96
1.9055-2.02490.22081210.18092443X-RAY DIFFRACTION98
2.0249-2.18130.20361160.15212424X-RAY DIFFRACTION98
2.1813-2.40070.18771350.14712469X-RAY DIFFRACTION99
2.4007-2.74810.17911260.15412481X-RAY DIFFRACTION100
2.7481-3.4620.1961370.15442534X-RAY DIFFRACTION100
3.462-41.92090.17311500.15822685X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.03371.4162.6772.46351.8624.02840.0331-0.08570.09080.1042-0.10590.23850.1106-0.13520.05480.11620.0270.00950.2035-0.0090.1959-16.1091-11.2182-14.8399
25.0762-4.1843-4.52964.2562.80855.18360.05840.50750.1802-0.3091-0.086-0.33010.1677-0.091-0.0820.2442-0.00660.01780.2698-0.01270.2028-2.5005-23.583-28.2134
33.2663-1.3220.37354.6169-0.09833.15560.06120.304-0.4236-0.24130.08010.36490.2794-0.39240.02850.1792-0.0276-0.03670.2356-0.03960.1872-15.8012-25.99-22.12
43.2567-0.3214-0.09943.97610.62234.0593-0.0614-0.0701-0.47970.20650.03160.13880.4846-0.20150.05380.20970.0016-0.00040.15360.00180.218-8.0036-29.2526-17.0456
53.613-0.5953-0.4852.41942.55622.70750.11740.1416-0.4389-0.0447-0.1029-0.59330.56910.141-0.05970.33850.06470.03080.16250.00290.2068-2.5981-29.2544-18.9956
63.0692-1.4264-4.1764.30013.21556.8652-0.2585-0.1682-0.27990.51640.0570.26220.70050.07580.14870.1786-0.01410.01340.18990.01040.1761-7.0375-24.448-2.9907
72.33510.3261.10391.6572-0.37453.5012-0.10760.11910.19950.0407-0.02220.0488-0.1480.21250.15960.0742-0.00230.02090.14450.00550.1187-4.0614-10.8078-15.4307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 265 )
4X-RAY DIFFRACTION4chain 'A' and (resid 266 through 298 )
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 309 )
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 328 )
7X-RAY DIFFRACTION7chain 'A' and (resid 329 through 379 )

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